Prostatic carcinoma is an important cancer in both men and dogs. Dogs have been a valuable animal model for investigating prostate cancer, but their relevance is unclear as the origin of canine prostatic carcinomas is unknown. We hypothesized that a proteomic approach for diagnosis of these neoplasms might provide quantitative data useful for more complete characterization of their origin. Protein expression profiles were prepared from normal canine prostate glands and bladders. The normal protein profiles were then compared with protein expression profiles of three canine prostatic carcinomas. Two-dimensional differential in-gel electrophoresis (2-D DIGE) was used to analyse an average of approximately 1000 proteins per carcinoma. When compared with normal prostate tissue, the carcinomas exhibited greater than 2.5-fold difference in expression for an average of 230 proteins. Similar proteomic comparisons between the carcinomas and the normal bladder revealed a greater than 2.5-fold difference in expression for an average of 208 proteins. Mass spectrometry and protein database homology were used to identify nine proteins (alpha-enolase, vimentin, GRP78, endoplasmin (GRP94), albumin, keratins 7 and 8, haptoglobin, and transferrin) overexpressed by the carcinomas. Statistical testing demonstrated that keratin 7, GRP78, and endoplasmin were significantly overexpressed in the carcinomas compared with normal prostate or bladder. Principal components analysis revealed that the carcinomas formed a unique cluster distinct from either the normal prostate or normal bladder. In conclusion, proteomic analysis revealed that whereas the majority of proteins expressed by canine prostatic carcinomas are also expressed by normal and neoplastic bladder and prostate tissue, the carcinomas contained unique protein components that allowed their segregation as a distinct group separate from normal canine prostate and bladder. Additionally, several proteins uniquely expressed by canine prostatic carcinomas were also identified.